A factory runs riot

Published March 01 2017

By Catherine Goodman

Locations where the bacterial strains were collected.

Bacteria are at war. Their foes? Other microorganisms. Their weapons? Among other things, they deploy small chemicals called natural products. These chemicals often are co-opted by humans for drugs, making it important to keep identifying natural products and the pathways by which they’re made. While these biosynthetic pathways often have minor departures from rules developed over many examples, a recent paper in the Journal of Biological Chemistry reports an extreme case of rule-breaking that explains how a structurally diverse group of natural products, called thalassospiramides, is made.

Two of the common pathways that bacteria use to make natural products rely on a series of enzymes linked together in long chains. The chained enzymes function much like factory workers at an assembly line: When a molecule arrives at their station, they add a new piece or adjust an existing piece and send it along. In this way, many copies of the same thing are made efficiently.

However, the bacterial foe doesn’t just sit around, waiting to be killed; the bacteria evolve to resist specific natural products. So many assembly lines either swap workers with other pathways or get the workers to make tweaks to create multiple, slightly different molecules based on the same overall blueprint.

A team led by Pei-Yuan Qian at Hong Kong University of Science and Technology and Bradley Moore at the University of California, San Diego previously had teamed up to study the assembly line that makes thalassospiramides. These compounds inhibit an enzyme called calpain protease, which is important in neurological disorders, cancer and other medical conditions.

In earlier work, Qian, Moore and colleagues reported 14 thalassospiramides from four types of ocean-dwelling bacteria. They also wanted to determine the blueprint for the assembly line because, as Qian recalls, “We wondered how and why bacteria from different genera produce similar compounds.”

Surprisingly, the assembly line was sending some workers home for the day, asking other workers to perform their jobs two or three times, and bringing in workers from elsewhere in the factory. As first author and then-postdoctoral fellow Avena Ross recalls, “The huge diversity of molecules seemed to be coming from a single, quite simple assembly line that behaved in a highly unusual manner.”

Since their first study only examined four bacteria, teams led by Qian, Moore and Ross — now a faculty member at Queen’s University — suspected there might be more to learn. So they looked through the Marine Culture Collection of China, including samples from the Baltic and Bering seas, the coasts of Madagascar and New Zealand, and everywhere in between, to assemble 130 different strains of bacteria, leading to 21 new thalassospiramides.

By looking at the DNA sequences for a subset of the bacteria they collected, the authors found seven copies of the thalassospiramide assembly line, only four of which were operational. By pairing compound structures with assembly lines, the authors could see how the four functional lines were hiring, firing and reusing enzymes even more than anticipated based on the previous report. Moreover, they discovered that attempts to outsource an intact assembly line to a different bacterial factory might have caused the seemingly functional but unproductive lines, as some of the individual parts needed for the assembly line workers weren’t available in the new factory.

While some of these individual mechanisms of hiring, firing and reusing enzymes to create compound diversity have been seen in other natural product assembly lines, the new mechanisms as well as their combination are surprising. Moore notes that the assembly line “is able to break so many of the conventional ‘rules.’”

Ross believes more surprises await as they determine how the rule-breaking occurs at the level of individual enzymes and reactions. Perhaps, in times of war, rules are meant to be broken.